tests/testthat/test-15-sparse.R

In tractor.base: Read, Manipulate and Visualise Magnetic Resonance Images

context("Sparse images")

reportr::setOutputLevel(Warning)
options(reportrStderrLevel=reportr::OL$Fatal)

test_that("we can read and work with sparse images", {
    imagePath <- system.file("extdata", "nifti", "maskedb0.nii.gz", package="tractor.base")
    boxesPath <- system.file("extdata", "nifti", "boxes.nii.gz", package="tractor.base")
    image <- readImageFile(imagePath)
    boxes <- readImageFile(boxesPath, sparse=TRUE)
    locs <- boxes$getNonzeroIndices()
    
    expect_true(boxes$isSparse())
    expect_equal(nrow(locs), 1072)
    expect_equal(1-boxes$getSparseness(), nrow(locs)/prod(dim(boxes)))
    expect_equal(round(mean(image[boxes])), 476)
    
    data <- boxes$getData()
    array <- as.array(boxes)
    expect_true(is(data, "SparseArray"))
    expect_equal(boxes[locs], data$getData())
    expect_equal(locs, data$getCoordinates())
    expect_equal(data$apply(1:2,max), apply(array,1:2,max))
    
    expect_equal(data[40,40,28], 1L)
    data[40,40,28] <- 0L
    expect_equal(data[40,40,28], 0L)
    expect_equal(length(data$getData()), nrow(locs)-1)
    data[locs] <- 0L
    expect_equal(dim(data$getCoordinates()), c(0L,3L))
    expect_equal(data$getData(), integer(0))
})